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Jun SE, Cho KH, Schaffrath R, Kim GT. Evolutionary Conservation in Protein-Protein Interactions and Structures of the Elongator Sub-Complex ELP456 from Arabidopsis and Yeast. Int J Mol Sci 2024; 25:4370. [PMID: 38673955 PMCID: PMC11050213 DOI: 10.3390/ijms25084370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The Elongator complex plays a pivotal role in the wobble uridine modification of the tRNA anticodon. Comprising two sets of six distinct subunits, namely, Elongator proteins (ELP1-ELP6) and associated proteins, the holo-Elongator complex demonstrates remarkable functional and structural conservation across eukaryotes. However, the precise details of the evolutionary conservation of the holo-Elongator complex and its individual sub-complexes (i.e., ELP123; ELP456) in plants remain limited. In this study, we conducted an in vivo analysis of protein-protein interactions among Arabidopsis ELP4, ELP5, and ELP6 proteins. Additionally, we predicted their structural configurations and performed a comparative analysis with the structure of the yeast Elp456 sub-complex. Protein-protein interaction analysis revealed that AtELP4 interacts with AtELP6 but not directly with AtELP5. Furthermore, we found that the Arabidopsis Elongator-associated protein, Deformed Roots and Leaves 1 (DRL1), did not directly bind to AtELP proteins. The structural comparison of the ELP456 sub-complex between Arabidopsis and yeast demonstrated high similarity, encompassing the RecA-ATPase fold and the positions of hydrogen bonds, despite their relatively low sequence homology. Our findings suggest that Arabidopsis ELP4, ELP5, and ELP6 proteins form a heterotrimer, with ELP6 serving as a bridge, indicating high structural conservation between the ELP456 sub-complexes from Arabidopsis and yeast.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
| | - Kiu-Hyung Cho
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Gyeongbuk Institute for Bioindustry, Andong 36618, Republic of Korea
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany;
| | - Gyung-Tae Kim
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Graduate School of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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Guo F, Islam MA, Lv C, Jin X, Sun L, Zhao K, Lu J, Yan R, Zhang W, Shi Y, Li N, Sun D. Insights into the Bioinformatics and Transcriptional Analysis of the Elongator Complexes ( ELPs) Gene Family of Wheat: TaELPs Contribute to Wheat Abiotic Stress Tolerance and Leaf Senescence. PLANTS (BASEL, SWITZERLAND) 2023; 12:952. [PMID: 36840300 PMCID: PMC9961319 DOI: 10.3390/plants12040952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Elongator complexes (ELPs) are the protein complexes that promote transcription through histone acetylation in eukaryotic cells and interact with elongating RNA polymerase II (RNAPII). ELPs' role in plant growth and development, signal transduction, and response to biotic and abiotic stresses have been confirmed in model plants. However, the functions of the wheat ELP genes are not well documented. The present study identified 18 members of the ELPs from the wheat genome with a homology search. Further, bioinformatics and transcription patterns in response to different stress conditions were analyzed to dissect their potential regulatory mechanisms in wheat. Gene duplication analysis showed that 18 pairs of ELP paralogous genes were derived from segmental duplication, which was divided into six clades by protein phylogenetic and cluster analysis. The orthologous analysis of wheat TaELP genes showed that TaELP genes may have evolved from orthologous genes of other plant species or closely related plants. Moreover, a variety of cis-acting regulatory elements (CAREs) related to growth and development, hormone response, and biotic and abiotic stresses were identified in the TaELPs' promoter regions. The qRT-PCR analysis showed that the transcription of TaELPs was induced under hormone, salt, and drought stress and during leaf senescence. The TaELP2 gene was silenced with BSMV-VIGS, and TaELP2 was preliminarily verified to be involved in the regulation of wheat leaf senescence. Overall, TaELP genes might be regulated by hormone signaling pathways and response to abiotic stress and leaf senescence, which could be investigated further as potential candidate genes for wheat abiotic stress tolerance and yield improvement.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Md Ashraful Islam
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
- Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA
| | - Chenxu Lv
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Xiujuan Jin
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Lili Sun
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Kai Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Juan Lu
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Rongyue Yan
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Wenjun Zhang
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Yugang Shi
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Ning Li
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Daizhen Sun
- State Key Laboratory of Sustainable Dryland Agriculture, College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
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Jun SE, Cho KH, Manzoor MA, Hwang TY, Kim YS, Schaffrath R, Kim GT. AtELP4 a subunit of the Elongator complex in Arabidopsis, mediates cell proliferation and dorsoventral polarity during leaf morphogenesis. FRONTIERS IN PLANT SCIENCE 2022; 13:1033358. [PMID: 36340367 PMCID: PMC9634574 DOI: 10.3389/fpls.2022.1033358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
The Elongator complex in eukaryotes has conserved tRNA modification functions and contributes to various physiological processes such as transcriptional control, DNA replication and repair, and chromatin accessibility. ARABIDOPSIS ELONGATOR PROTEIN 4 (AtELP4) is one of the six subunits (AtELP1-AtELP6) in Arabidopsis Elongator. In addition, there is an Elongator-associated protein, DEFORMED ROOTS AND LEAVES 1 (DRL1), whose homolog in yeast (Kti12) binds tRNAs. In this study, we explored the functions of AtELP4 in plant-specific aspects such as leaf morphogenesis and evolutionarily conserved ones between yeast and Arabidopsis. ELP4 comparison between yeast and Arabidopsis revealed that plant ELP4 possesses not only a highly conserved P-loop ATPase domain but also unknown plant-specific motifs. ELP4 function is partially conserved between Arabidopsis and yeast in the growth sensitivity toward caffeine and elevated cultivation temperature. Either single Atelp4 or drl1-102 mutants and double Atelp4 drl1-102 mutants exhibited a reduction in cell proliferation and changed the adaxial-abaxial polarity of leaves. In addition, the single Atelp4 and double Atelp4 drl1-102 mutants showed remarkable downward curling at the whole part of leaf blades in contrast to wild-type leaf blades. Furthermore, our genetic study revealed that AtELP4 might epistatically act on DRL1 in the regulation of cell proliferation and dorsoventral polarity in leaves. Taken together, we suggest that AtELP4 as part of the plant Elongator complex may act upstream of a regulatory pathway for adaxial-abaxial polarity and cell proliferation during leaf development.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan, South Korea
| | - Kiu-Hyung Cho
- Department of Molecular Genetics, Dong-A University, Busan, South Korea
| | | | - Tae Young Hwang
- Graduate School of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Youn Soo Kim
- Graduate School of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Gyung-Tae Kim
- Department of Molecular Genetics, Dong-A University, Busan, South Korea
- Graduate School of Applied Bioscience, Dong-A University, Busan, South Korea
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Myat AA, Zhou Y, Gao Y, Zhao X, Liang C, Abid MA, Wang P, Akram U, Abbas M, Askari M, Guo S, Zhang R, Meng Z. Overexpression of GhKTI12 Enhances Seed Yield and Biomass Production in Nicotiana Tabacum. Genes (Basel) 2022; 13:426. [PMID: 35327981 PMCID: PMC8953243 DOI: 10.3390/genes13030426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/04/2023] Open
Abstract
Crop molecular breeding primarily focuses on increasing the trait of plant yield. An elongator-associated protein, KTI12, is closely associated with plant biomass and yield. KTI12 is involved in developmental processes of most organs, including the leaf, root, flower, and seed, through regulating cell division and differentiation. Previous work has shown that in upland cotton (Gossypium hirsutum), GhKTI12 regulates plant height, flowering, and tolerance to salt and drought stress. However, little is known about the molecular regulation mechanism of GhKTI12 in plant developmental processes. In this study, we identified the main GhKTI12 (Gh_D02G144400) gene and transformed it into tobacco (Nicotonia tabacum cv NC89). From seven transgenic lines, we obtained three (OE5, OE6 and OE8) with high expression of GhKTI12; compared with wild type plants, these three lines exhibited larger plant size, later flowering, and higher seed yield. Microscopic observation revealed that the number of leaf epidermal cells and stem parenchyma cells was increased by ~55%. Biochemical analysis showed that chlorophyll content and starch accumulation were significantly increased in younger leaves at the top canopy of transgenic plants, which may contribute to improved photosynthetic rate and, in turn, increased seed yield. To understand the molecular mechanism of GhKTI12 in transgenic plants development, two lines (OE6 and OE8) with higher expression levels of GhKTI12 were used as representative plants to conduct RNA-seq analysis. Through transcriptome analysis of the plant's shoot apical meristematic tissue of these two lines, we identified 518 upregulated genes and 406 downregulated genes common to both overexpression lines. A large number of cellular component genes associated with cell division and differentiation, such as RD21, TET8, KTN80, AOX1, AOX2, CP1, and KIC, were found to be upregulated, and genes showing the most downregulation included MADS-box genes related to flowering time, such as MADS6, AP1, AP3, AGL8, AGL6, SEP1, and SEP2. Downregulation of these genes caused delayed flowering time and longer vegetative stage during development. Combined with the upregulation of the yield-related gene RD21, the GhKTI12 transgenic plants could produce a higher seed yield. We here show that the overexpression of GhKTI12 could positively improve key agronomic traits in tobacco by regulating cell proliferation, photosynthesis, and organ development, and suggest that homologs of GhKTI12 may also be important in the genetic improvement of other crop plants.
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Affiliation(s)
- Aye Aye Myat
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Yu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Yuan Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Xiang Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Umar Akram
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
- Institute of Plant Breeding and Biotechnology, MNS—University of Agriculture, Multan 60000, Pakistan
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Muhammad Askari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.A.M.); (Y.Z.); (Y.G.); (X.Z.); (C.L.); (M.A.A.); (P.W.); (U.A.); (M.A.); (M.A.); (S.G.); (R.Z.)
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5
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Tavares JF, Davis NK, Poim A, Reis A, Kellner S, Sousa I, Soares AR, Moura GMR, Dedon PC, Santos M. tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. RNA Biol 2021; 18:563-575. [PMID: 32893724 PMCID: PMC7971265 DOI: 10.1080/15476286.2020.1819671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/28/2023] Open
Abstract
Protein synthesis rate and accuracy are tightly controlled by the cell and are essential for proteome homoeostasis (proteostasis); however, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood. To address this question, we evaluated the role of 70 yeast tRNA-modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated proteins. We show that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, the mitochondrial tRNA-modifying enzyme Slm3 plays a fundamental role in general proteostasis and that stress response proteins whose genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications are overrepresented in protein aggregates of the ELP1, SLM3 and TRM9 KO strains. Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.
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Affiliation(s)
- Joana F Tavares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Nick K. Davis
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Ana Poim
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Andreia Reis
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Inês Sousa
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana R. Soares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela M R Moura
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise – CREATE, Singapore
| | - Manuel Santos
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
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Smejda M, Kądziołka D, Radczuk N, Krutyhołowa R, Chramiec-Głąbik A, Kędracka-Krok S, Jankowska U, Biela A, Glatt S. Same but different - Molecular comparison of human KTI12 and PSTK. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:118945. [PMID: 33417976 DOI: 10.1016/j.bbamcr.2020.118945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022]
Abstract
Kti12 and PSTK are closely related and highly similar proteins implicated in different aspects of tRNA metabolism. Kti12 has been identified as an essential regulatory factor of the Elongator complex, involved in the modification of uridine bases in eukaryotic tRNAs. PSTK phosphorylates the tRNASec-bound amino acid serine, which is required to synthesize selenocysteine. Kti12 and PSTK have previously been studied independently in various organisms, but only appear simultaneously in some animalia, including humans. As Kti12- and PSTK-related pathways are clinically relevant, it is of prime importance to understand their biological functions and mutual relationship in humans. Here, we use different tRNA substrates to directly compare the enzymatic activities of purified human KTI12 and human PSTK proteins. Our complementary Co-IP and BioID2 approaches in human cells confirm that Elongator is the main interaction partner of KTI12 but additionally indicate potential links to proteins involved in vesicular transport, RNA metabolism and deubiquitination. Moreover, we identify and validate a yet uncharacterized interaction between PSTK and γ-taxilin. Foremost, we demonstrate that human KTI12 and PSTK do not share interactors or influence their respective biological functions. Our data provide a comprehensive analysis of the regulatory networks controlling the activity of the human Elongator complex and selenocysteine biosynthesis.
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Affiliation(s)
- Marta Smejda
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dominika Kądziołka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Natalia Radczuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Sylwia Kędracka-Krok
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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Wang H, Xu C, Zhang Y, Yan X, Jin X, Yao X, Chen P, Zheng B. PtKTI12 genes influence wobble uridine modifications and drought stress tolerance in hybrid poplar. TREE PHYSIOLOGY 2020; 40:1778-1791. [PMID: 32705117 DOI: 10.1093/treephys/tpaa088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
The multisubunit Elongator complex plays key roles in transcription by interacting with RNA polymerase II and chromatin modeling. Kti proteins have been identified as the auxiliary protein for the Elongator complex. However, our knowledge of Kti proteins in woody plants remains limited. In this study, in total 16 KTI gene homologs were identified in Populus trichocarpa. Among them, the two KTI12 candidates were named PtKTI12A and PtKTI12B. Although PtKTI12A and PtKTI12B were largely different in gene expression level and tissue specificity, both genes were induced by heat and drought stresses. PtKTI12A and PtKTI12B RNAi transgenic poplar plants showed reduced levels of modified nucleosides, in particular 5-carbamoylmethyluridine and 5-methoxycarbonylmethyl-2-thiouridine. Meanwhile, their tolerance to drought was improved when subjected to withdrawal of watering. Also, the protein products of PtKTI12A and PtKTI12B had similar subcellular localization and predicted tertiary structure. The results suggest that Kti12 proteins are involved in tRNA wobble uridine modification, stress response and drought stress tolerance in hybrid poplar.
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Affiliation(s)
- Hailang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Xueyuan Rd, Wuhan 430070, China
| | - Chao Xu
- Yuan Longping High-Tech Agriculture Co. Ltd., No. 638, Heping Rd, Changsha 410001, China
| | - Youbing Zhang
- Guangzhou Vipotion Biotechnology Co. Ltd., 5F, Building J5, No.1 Jiantashan Road, Guangzhou Science Park, Guangzhou 510663, China
| | - Xu Yan
- Shacheng Middle School, Longtan W St, Zhangjiakou 075000, China
| | - Xiaohuan Jin
- College of Plant Science and Technology, Huazhong Agricultural University, Xueyuan Rd, Wuhan 430070, China
| | - Xiaoqing Yao
- College of Plant Science and Technology, Huazhong Agricultural University, Xueyuan Rd, Wuhan 430070, China
| | - Peng Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Xueyuan Rd, Wuhan 430070, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticultural and Forestry Sciences, Huazhong Agricultural University, Xueyuan Rd, Wuhan 430070, China
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8
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Krutyhołowa R, Reinhardt-Tews A, Chramiec-Głąbik A, Breunig KD, Glatt S. Fungal Kti12 proteins display unusual linker regions and unique ATPase p-loops. Curr Genet 2020; 66:823-833. [PMID: 32236652 PMCID: PMC7363723 DOI: 10.1007/s00294-020-01070-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022]
Abstract
Kti12 (Kluyveromyces lactis toxin insensitive 12) is an evolutionary highly conserved ATPase, crucial for the tRNA-modification activity of the eukaryotic Elongator complex. The protein consists of an N-terminal ATPase and a C-terminal tRNA-binding domain, which are connected by a flexible linker. The precise role of the linker region and its involvement in the communication between the two domains and their activities remain elusive. Here, we analyzed all available Kti12 protein sequences and report the discovery of a subset of Kti12 proteins with abnormally long linker regions. These Kti12 proteins are characterized by a co-occurring lysine to leucine substitution in their Walker A motif, previously thought to be invariable. We show that the K14L substitution lowers the affinity to ATP, but does not affect the catalytic activity of Kti12 at high ATP concentrations. We compare the activity of mutated variants of Kti12 in vitro with complementation assays in vivo in yeast. Ultimately, we compared Kti12 to other known p-loop ATPase family members known to carry a similar deviant Walker A motif. Our data establish Kti12 of Eurotiomycetes as an example of eukaryotic ATPase harboring a significantly deviating but still functional Walker A motif.
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Affiliation(s)
- Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | | | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer. Genes (Basel) 2018; 10:genes10010019. [PMID: 30597914 PMCID: PMC6356722 DOI: 10.3390/genes10010019] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA modifications in prevention of neurodegeneration, certain cancer types upregulate tRNA modification genes to sustain cancer cell gene expression and metastasis. Multiple associations of defects in genes encoding subunits of the tRNA modifier complex Elongator with human disease highlight the importance of proper anticodon wobble uridine modifications (xm⁵U34) for health. Elongator functionality requires communication with accessory proteins and dynamic phosphorylation, providing regulatory control of its function. Here, we summarized recent insights into molecular functions of the complex and the role of Elongator dependent tRNA modification in human disease.
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10
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Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Genetic analysis reveals functions of atypical polyubiquitin chains. eLife 2018; 7:42955. [PMID: 30547882 PMCID: PMC6305200 DOI: 10.7554/elife.42955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Although polyubiquitin chains linked through all lysines of ubiquitin exist, specific functions are well-established only for lysine-48 and lysine-63 linkages in Saccharomyces cerevisiae. To uncover pathways regulated by distinct linkages, genetic interactions between a gene deletion library and a panel of lysine-to-arginine ubiquitin mutants were systematically identified. The K11R mutant had strong genetic interactions with threonine biosynthetic genes. Consistently, we found that K11R mutants import threonine poorly. The K11R mutant also exhibited a strong genetic interaction with a subunit of the anaphase-promoting complex (APC), suggesting a role in cell cycle regulation. K11-linkages are important for vertebrate APC function, but this was not previously described in yeast. We show that the yeast APC also modifies substrates with K11-linkages in vitro, and that those chains contribute to normal APC-substrate turnover in vivo. This study reveals comprehensive genetic interactomes of polyubiquitin chains and characterizes the role of K11-chains in two biological pathways.
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Affiliation(s)
- Fernando Meza Gutierrez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Arda Mizrak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Raquel Tamse-Kuehn
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Curt Palm
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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11
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Wang C, Zhang X, Li J, Zhang Y, Mou Z. The Elongator complex-associated protein DRL1 plays a positive role in immune responses against necrotrophic fungal pathogens in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2018; 19:286-299. [PMID: 27868335 PMCID: PMC6637984 DOI: 10.1111/mpp.12516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 05/24/2023]
Abstract
DEFORMED ROOT AND LEAVES1 (DRL1) is an Arabidopsis homologue of the yeast TOXIN TARGET4 (TOT4)/KILLER TOXIN-INSENSITIVE12 (KTI12) protein that is physically associated with the RNA polymerase II-interacting protein complex named Elongator. Mutations in DRL1 and Elongator lead to similar morphological and molecular phenotypes, suggesting that DRL1 and Elongator may functionally overlap in Arabidopsis. We have shown previously that Elongator plays an important role in both salicylic acid (SA)- and jasmonic acid (JA)/ethylene (ET)-mediated defence responses. Here, we tested whether DRL1 also plays a similar role as Elongator in plant immune responses. Our results show that, although DRL1 partially contributes to SA-induced cytotoxicity, it does not play a significant role in SA-mediated expression of PATHOGENESIS-RELATED genes and resistance to the virulent bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. In contrast, DRL1 is required for JA/ET- and necrotrophic fungal pathogen Botrytis cinerea-induced defence gene expression and for resistance to B. cinerea and Alternaria brassicicola. Furthermore, unlike the TOT4/KTI12 gene which, when overexpressed in yeast, confers zymocin resistance, a phenotype of the tot4/kti12 mutant, overexpression of DRL1 does not change B. cinerea-induced defence gene expression and resistance to this pathogen. Finally, DRL1 contains an N-terminal P-loop and a C-terminal calmodulin (CaM)-binding domain and is a CaM-binding protein. We demonstrate that both the P-loop and the CaM-binding domain are essential for the function of DRL1 in B. cinerea-induced expression of PDF1.2 and ORA59, and in resistance to B. cinerea, suggesting that the function of DRL1 in plant immunity may be regulated by ATP/GTP and CaM binding.
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Affiliation(s)
- Chenggang Wang
- Department of Microbiology and Cell ScienceUniversity of Florida, PO Box 110700GainesvilleFL32611USA
| | - Xudong Zhang
- Department of Microbiology and Cell ScienceUniversity of Florida, PO Box 110700GainesvilleFL32611USA
| | - Jian‐Liang Li
- Sanford Burnham Prebys Medical Discovery Institute at Lake NonaOrlandoFL32827USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622GainesvilleFL32610USA
| | - Zhonglin Mou
- Department of Microbiology and Cell ScienceUniversity of Florida, PO Box 110700GainesvilleFL32611USA
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12
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Mehlgarten C, Prochaska H, Hammermeister A, Abdel-Fattah W, Wagner M, Krutyhołowa R, Jun SE, Kim GT, Glatt S, Breunig KD, Stark MJR, Schaffrath R. Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator. Toxins (Basel) 2017; 9:E272. [PMID: 28872616 PMCID: PMC5618205 DOI: 10.3390/toxins9090272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/29/2017] [Accepted: 09/03/2017] [Indexed: 01/23/2023] Open
Abstract
Saccharomyces cerevisiae cells are killed by zymocin, a tRNase ribotoxin complex from Kluyveromyces lactis, which cleaves anticodons and inhibits protein synthesis. Zymocin's action requires specific chemical modification of uridine bases in the anticodon wobble position (U34) by the Elongator complex (Elp1-Elp6). Hence, loss of anticodon modification in mutants lacking Elongator or related KTI (K. lactis Toxin Insensitive) genes protects against tRNA cleavage and confers resistance to the toxin. Here, we show that zymocin can be used as a tool to genetically analyse KTI12, a gene previously shown to code for an Elongator partner protein. From a kti12 mutant pool of zymocin survivors, we identify motifs in Kti12 that are functionally directly coupled to Elongator activity. In addition, shared requirement of U34 modifications for nonsense and missense tRNA suppression (SUP4; SOE1) strongly suggests that Kti12 and Elongator cooperate to assure proper tRNA functioning. We show that the Kti12 motifs are conserved in plant ortholog DRL1/ELO4 from Arabidopsis thaliana and seem to be involved in binding of cofactors (e.g., nucleotides, calmodulin). Elongator interaction defects triggered by mutations in these motifs correlate with phenotypes typical for loss of U34 modification. Thus, tRNA modification by Elongator appears to require physical contact with Kti12, and our preliminary data suggest that metabolic signals may affect proper communication between them.
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Affiliation(s)
- Constance Mehlgarten
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Heike Prochaska
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Alexander Hammermeister
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Heirich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Heirich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Melanie Wagner
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Krakow, Poland.
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 31-007 Krakow, Poland.
| | - Sang Eun Jun
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714, Korea.
| | - Gyung-Tae Kim
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714, Korea.
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Krakow, Poland.
| | - Karin D Breunig
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Michael J R Stark
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Raffael Schaffrath
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Heirich-Plett-Str. 40, 34132 Kassel, Germany.
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13
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Abstract
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA. Finally, we discuss how defects in wobble uridine modifications lead to phenotypes in different species. Importantly, this review will mainly focus on the cytoplasmic tRNAs of eukaryotes. A recent review has extensively covered their bacterial and mitochondrial counterparts.1
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Affiliation(s)
- Raffael Schaffrath
- a Institut für Biologie, FG Mikrobiologie , Universität Kassel , Germany
| | - Sebastian A Leidel
- b Max Planck Institute for Molecular Biomedicine , Germany.,c Cells-in-Motion Cluster of Excellence , University of Münster , Münster , Germany.,d Medical Faculty , University of Münster , Albert-Schweitzer-Campus 1, Münster , Germany
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14
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Zhou H, Liu Q, Shi T, Yu Y, Lu H. Genome-wide screen of fission yeast mutants for sensitivity to 6-azauracil, an inhibitor of transcriptional elongation. Yeast 2015; 32:643-55. [DOI: 10.1002/yea.3085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/23/2015] [Accepted: 06/26/2015] [Indexed: 01/10/2023] Open
Affiliation(s)
- Huan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Qi Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing Technology; Shanghai 200237 People's Republic of China
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15
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Jun SE, Cho KH, Hwang JY, Abdel-Fattah W, Hammermeister A, Schaffrath R, Bowman JL, Kim GT. Comparative analysis of the conserved functions of Arabidopsis DRL1 and yeast KTI12. Mol Cells 2015; 38:243-50. [PMID: 25518926 PMCID: PMC4363724 DOI: 10.14348/molcells.2015.2297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 12/18/2022] Open
Abstract
Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1-101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | - Kiu-Hyung Cho
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | - Ji-Young Hwang
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel,
Germany
| | | | - Raffael Schaffrath
- Department of Genetics, University of Leicester,
UK
- Institut für Biologie, FG Mikrobiologie, Universität Kassel,
Germany
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne,
Australia
| | - Gyung-Tae Kim
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
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16
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Abdel-Fattah W, Jablonowski D, Di Santo R, Thüring KL, Scheidt V, Hammermeister A, ten Have S, Helm M, Schaffrath R, Stark MJR. Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast. PLoS Genet 2015; 11:e1004931. [PMID: 25569479 PMCID: PMC4287497 DOI: 10.1371/journal.pgen.1004931] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/01/2014] [Indexed: 12/26/2022] Open
Abstract
Elongator is a conserved protein complex comprising six different polypeptides that has been ascribed a wide range of functions, but which is now known to be required for modification of uridine residues in the wobble position of a subset of tRNAs in yeast, plants, worms and mammals. In previous work, we showed that Elongator's largest subunit (Elp1; also known as Iki3) was phosphorylated and implicated the yeast casein kinase I Hrr25 in Elongator function. Here we report identification of nine in vivo phosphorylation sites within Elp1 and show that four of these, clustered close to the Elp1 C-terminus and adjacent to a region that binds tRNA, are important for Elongator's tRNA modification function. Hrr25 protein kinase directly modifies Elp1 on two sites (Ser-1198 and Ser-1202) and through analyzing non-phosphorylatable (alanine) and acidic, phosphomimic substitutions at Ser-1198, Ser-1202 and Ser-1209, we provide evidence that phosphorylation plays a positive role in the tRNA modification function of Elongator and may regulate the interaction of Elongator both with its accessory protein Kti12 and with Hrr25 kinase. tRNA molecules function as adapters in protein synthesis, bringing amino acids to the ribosome and reading the genetic code through codon-anticodon base pairing. When the tRNA contains a uridine residue in the “wobble position” of its anticodon, which base-pairs with purine residues in the third position of a cognate codon, it is almost always chemically modified and modification is required for efficient decoding. In eukaryotic cells, these wobble uridine modifications require a conserved protein complex called Elongator. Our work shows that Elp1, Elongator's largest subunit, is phosphorylated on several sites. By blocking phosphorylation at these positions using mutations, we identified four phosphorylation sites that are important for Elongator's role in tRNA modification. We have also shown that Hrr25 protein kinase, a member of the casein kinase I (CKI) family, is responsible for modification of two of the sites that are important for Elongator function. Phosphorylation appears to affect interaction of the Elongator complex both with its kinase (Hrr25) and with Kti12, an accessory protein previously implicated in Elongator function. Our studies imply that Elp1 phosphorylation plays a positive role in Elongator-mediated tRNA modification and raise the possibility that wobble uridine modification may be regulated, representing a potential translational control mechanism.
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Affiliation(s)
- Wael Abdel-Fattah
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Rachael Di Santo
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kathrin L. Thüring
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Viktor Scheidt
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Sara ten Have
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail: (RS); (MJRS)
| | - Michael J. R. Stark
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail: (RS); (MJRS)
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17
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A novel Sit4 phosphatase complex is involved in the response to ceramide stress in yeast. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:129645. [PMID: 24082981 PMCID: PMC3777123 DOI: 10.1155/2013/129645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/28/2013] [Accepted: 07/25/2013] [Indexed: 12/17/2022]
Abstract
Ceramide is a building block for complex sphingolipids in the plasma membrane, but it also plays a significant role in secondary signalling pathways regulating cell proliferation and apoptosis in response to stress. Ceramide activated protein phosphatase activity has been previously observed in association with the Sit4 protein phosphatase. Here we find that sit4Δ mutants have decreased ceramide levels and display resistance to exogenous ceramides and phytosphingosine. Mutants lacking SIT4 or KTI12 display a shift towards nonhydroxylated forms of long chain bases and sphingolipids, suggesting regulation of hydroxylase (SUR2) or ceramide synthase by Sit4p. We have identified novel subunits of the Sit4 complex and have also shown that known Sit4 regulatory subunits—SAP proteins—are not involved in the ceramide response. This is the first observation of separation of function between Sit4 and SAP proteins. We also find that the Sit4p target Elongator is not involved in the ceramide response but that cells deficient in Kti12p—an accessory protein with an undefined regulatory role—have similar ceramide phenotypes to sit4Δ mutants. Therefore, Kti12p may play a similar secondary role in the ceramide response. This evidence points to a novel Sit4-dependent regulatory mechanism in response to ceramide stress.
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18
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Kaer K, Branovets J, Hallikma A, Nigumann P, Speek M. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation. PLoS One 2011; 6:e26099. [PMID: 22022525 PMCID: PMC3192792 DOI: 10.1371/journal.pone.0026099] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/19/2011] [Indexed: 12/30/2022] Open
Abstract
Background Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown. Methodology/Principal Findings Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3′ ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs) and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals. Conclusions/Significance Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.
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Affiliation(s)
- Kristel Kaer
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Jelena Branovets
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Anni Hallikma
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Pilvi Nigumann
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Mart Speek
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- * E-mail:
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19
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Chen C, Huang B, Anderson JT, Byström AS. Unexpected accumulation of ncm(5)U and ncm(5)S(2) (U) in a trm9 mutant suggests an additional step in the synthesis of mcm(5)U and mcm(5)S(2)U. PLoS One 2011; 6:e20783. [PMID: 21687733 PMCID: PMC3110198 DOI: 10.1371/journal.pone.0020783] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 05/09/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Transfer RNAs are synthesized as a primary transcript that is processed to produce a mature tRNA. As part of the maturation process, a subset of the nucleosides are modified. Modifications in the anticodon region often modulate the decoding ability of the tRNA. At position 34, the majority of yeast cytosolic tRNA species that have a uridine are modified to 5-carbamoylmethyluridine (ncm(5)U), 5-carbamoylmethyl-2'-O-methyluridine (ncm(5)Um), 5-methoxycarbonylmethyl-uridine (mcm(5)U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U). The formation of mcm(5) and ncm(5) side chains involves a complex pathway, where the last step in formation of mcm(5) is a methyl esterification of cm(5) dependent on the Trm9 and Trm112 proteins. METHODOLOGY AND PRINCIPAL FINDINGS Both Trm9 and Trm112 are required for the last step in formation of mcm(5) side chains at wobble uridines. By co-expressing a histidine-tagged Trm9p together with a native Trm112p in E. coli, these two proteins purified as a complex. The presence of Trm112p dramatically improves the methyltransferase activity of Trm9p in vitro. Single tRNA species that normally contain mcm(5)U or mcm(5)s(2)U nucleosides were isolated from trm9Δ or trm112Δ mutants and the presence of modified nucleosides was analyzed by HPLC. In both mutants, mcm(5)U and mcm(5)s(2)U nucleosides are absent in tRNAs and the major intermediates accumulating were ncm(5)U and ncm(5)s(2)U, not the expected cm(5)U and cm(5)s(2)U. CONCLUSIONS Trm9p and Trm112p function together at the final step in formation of mcm(5)U in tRNA by using the intermediate cm(5)U as a substrate. In tRNA isolated from trm9Δ and trm112Δ strains, ncm(5)U and ncm(5)s(2)U nucleosides accumulate, questioning the order of nucleoside intermediate formation of the mcm(5) side chain. We propose two alternative explanations for this observation. One is that the intermediate cm(5)U is generated from ncm(5)U by a yet unknown mechanism and the other is that cm(5)U is formed before ncm(5)U and mcm(5)U.
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Affiliation(s)
- Changchun Chen
- Department of Molecular Biology, Umeå
University, Umeå, Sweden
| | - Bo Huang
- Department of Molecular Biology, Umeå
University, Umeå, Sweden
- Division of Epidemiology, Department of
Medicine and Public Health, Vanderbilt University School of Medicine, Nashville,
Tennessee, United States of America
| | - James T. Anderson
- Department of Biological Sciences, Marquette
University, Milwaukee, Wisconsin, United States of America
- * E-mail: (JTA); (ASB)
| | - Anders S. Byström
- Department of Molecular Biology, Umeå
University, Umeå, Sweden
- * E-mail: (JTA); (ASB)
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Benschop JJ, Brabers N, van Leenen D, Bakker LV, van Deutekom HWM, van Berkum NL, Apweiler E, Lijnzaad P, Holstege FCP, Kemmeren P. A consensus of core protein complex compositions for Saccharomyces cerevisiae. Mol Cell 2010; 38:916-28. [PMID: 20620961 DOI: 10.1016/j.molcel.2010.06.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 04/02/2010] [Accepted: 05/16/2010] [Indexed: 11/28/2022]
Abstract
Analyses of biological processes would benefit from accurate definitions of protein complexes. High-throughput mass spectrometry data offer the possibility of systematically defining protein complexes; however, the predicted compositions vary substantially depending on the algorithm applied. We determine consensus compositions for 409 core protein complexes from Saccharomyces cerevisiae by merging previous predictions with a new approach. Various analyses indicate that the consensus is comprehensive and of high quality. For 85 out of 259 complexes not recorded in GO, literature search revealed strong support in the form of coprecipitation. New complexes were verified by an independent interaction assay and by gene expression profiling of strains with deleted subunits, often revealing which cellular processes are affected. The consensus complexes are available in various formats, including a merge with GO, resulting in 518 protein complex compositions. The utility is further demonstrated by comparison with binary interaction data to reveal interactions between core complexes.
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Affiliation(s)
- Joris J Benschop
- Department of Physiological Chemistry, University Medical Centre Utrecht, 3584 CG Utrecht, The Netherlands
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21
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Mehlgarten C, Jablonowski D, Wrackmeyer U, Tschitschmann S, Sondermann D, Jäger G, Gong Z, Byström AS, Schaffrath R, Breunig KD. Elongator function in tRNA wobble uridine modification is conserved between yeast and plants. Mol Microbiol 2010; 76:1082-94. [PMID: 20398216 PMCID: PMC2904499 DOI: 10.1111/j.1365-2958.2010.07163.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2010] [Indexed: 01/17/2023]
Abstract
Based on studies in yeast and mammalian cells the Elongator complex has been implicated in functions as diverse as histone acetylation, polarized protein trafficking and tRNA modification. Here we show that Arabidopsis mutants lacking the Elongator subunit AtELP3/ELO3 have a defect in tRNA wobble uridine modification. Moreover, we demonstrate that yeast elp3 and elp1 mutants expressing the respective Arabidopsis Elongator homologues AtELP3/ELO3 and AtELP1/ELO2 assemble integer Elongator complexes indicating a high degree of structural conservation. Surprisingly, in vivo complementation studies based on Elongator-dependent tRNA nonsense suppression and zymocin tRNase toxin assays indicated that while AtELP1 rescued defects of a yeast elp1 mutant, the most conserved Elongator gene AtELP3, failed to complement an elp3 mutant. This lack of complementation is due to incompatibility with yeast ELP1 as coexpression of both plant genes in an elp1 elp3 yeast mutant restored Elongator's tRNA modification function in vivo. Similarly, AtELP1, not ScELP1 also supported partial complementation by yeast-plant Elp3 hybrids suggesting that AtElp1 has less stringent sequence requirements for Elp3 than ScElp1. We conclude that yeast and plant Elongator share tRNA modification roles and propose that this function might be conserved in Elongator from all eukaryotic kingdoms of life.
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Affiliation(s)
- Constance Mehlgarten
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-WittenbergWeinbergweg 10, D-06120 Halle (Saale), Germany
| | - Daniel Jablonowski
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-WittenbergWeinbergweg 10, D-06120 Halle (Saale), Germany
| | - Uta Wrackmeyer
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-WittenbergWeinbergweg 10, D-06120 Halle (Saale), Germany
| | - Susan Tschitschmann
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-WittenbergWeinbergweg 10, D-06120 Halle (Saale), Germany
| | - David Sondermann
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-WittenbergWeinbergweg 10, D-06120 Halle (Saale), Germany
| | - Gunilla Jäger
- Department of Molecular Biology, Umea University90187 Umea, Sweden
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural UniversityBeijing 100094, China
| | - Anders S Byström
- Department of Molecular Biology, Umea University90187 Umea, Sweden
| | - Raffael Schaffrath
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-WittenbergWeinbergweg 10, D-06120 Halle (Saale), Germany
| | - Karin D Breunig
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-WittenbergWeinbergweg 10, D-06120 Halle (Saale), Germany
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Mehlgarten C, Jablonowski D, Breunig KD, Stark MJR, Schaffrath R. Elongator function depends on antagonistic regulation by casein kinase Hrr25 and protein phosphatase Sit4. Mol Microbiol 2009; 73:869-81. [PMID: 19656297 DOI: 10.1111/j.1365-2958.2009.06811.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In yeast, the role for the Elongator complex in tRNA anticodon modification is affected by phosphorylation of Elongator subunit Elp1. Thus, hyperphosphorylation of Elp1 due to inactivation of protein phosphatase Sit4 correlates with Elongator-minus phenotypes including resistance towards zymocin, a tRNase cleaving anticodons of Elongator-dependent tRNAs. Here we show that zymocin resistance of casein kinase hrr25 mutants associates with hypophosphorylation of Elp1 and that nonsense suppression by the Elongator-dependent SUP4 tRNA is abolished in hrr25 or sit4 mutants. Thus changes that perturb the evenly balanced ratio between hyper- and hypophosphorylated Elp1 forms present in wild-type cells lead to Elongator inactivation. Antagonistic roles for Hrr25 and Sit4 in Elongator function are further supported by our data that Sit4 inactivation is capable of restoring both zymocin sensitivity and normal ratios between the two Elp1 forms in hrr25 mutants. Hrr25 binds to Elongator in a fashion dependent on Elongator partner Kti12. Like sit4 mutants, overexpression of Kti12 triggers Elp1 hyperphosphorylation. Intriguingly, this effect of Kti12 is blocked by hrr25 mutations, which also show enhanced binding of Kti12 to Elongator. Collectively, our data suggest that rather than directly targeting Elp1, the Hrr25 kinase indirectly affects Elp1 phosphorylation states through control of Sit4-dependent dephosphorylation of Elp1.
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Affiliation(s)
- Constance Mehlgarten
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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23
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The tRNA modification complex elongator regulates the Cdc42-dependent mitogen-activated protein kinase pathway that controls filamentous growth in yeast. EUKARYOTIC CELL 2009; 8:1362-72. [PMID: 19633267 DOI: 10.1128/ec.00015-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Signal transduction pathways control multiple aspects of cellular behavior, including global changes to the cell cycle, cell polarity, and gene expression, which can result in the formation of a new cell type. In the budding yeast Saccharomyces cerevisiae, the mitogen-activated protein kinase (MAPK) pathway that controls filamentous growth induces a dimorphic foraging response under nutrient-limiting conditions. How nutritional cues feed into MAPK activation remains an open question. Here we report a functional connection between the elongator tRNA modification complex (ELP genes) and activity of the filamentous growth pathway. Elongator was required for filamentous growth pathway signaling, and elp mutants were defective for invasive growth, cell polarization, and MAPK-dependent mat formation. Genetic suppression analysis showed that elongator functions at the level of Msb2p, the signaling mucin that operates at the head of the pathway, which led to the finding that elongator regulates the starvation-dependent expression of the MSB2 gene. The Elp complex was not required for activation of related pathways (pheromone response or high osmolarity glycerol response) that share components with the filamentous growth pathway. Because protein translation provides a rough metric of cellular nutritional status, elongator may convey nutritional information to the filamentous growth pathway at the level of MSB2 expression.
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24
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Greenwood C, Selth LA, Dirac-Svejstrup AB, Svejstrup JQ. An Iron-Sulfur Cluster Domain in Elp3 Important for the Structural Integrity of Elongator. J Biol Chem 2009; 284:141-149. [DOI: 10.1074/jbc.m805312200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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25
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Huang B, Lu J, Byström AS. A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2008; 14:2183-94. [PMID: 18755837 PMCID: PMC2553728 DOI: 10.1261/rna.1184108] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We recently showed that the gamma-subunit of Kluyveromyces lactis killer toxin (gamma-toxin) is a tRNA endonuclease that cleaves tRNA(mcm5s2UUC Glu), tRNA(mcm5s2UUU Lys), and tRNA(mcm5s2UUG Gln) 3' of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U). The 5-methoxycarbonylmethyl (mcm(5)) side chain was important for efficient cleavage by gamma-toxin, and defects in mcm(5) side-chain synthesis correlated with resistance to gamma-toxin. Based on this correlation, a genome-wide screen was performed to identify gene products involved in the formation of the mcm(5) side chain. From a collection of 4826 homozygous diploid Saccharomyces cerevisiae strains, each with one nonessential gene deleted, 63 mutants resistant to Kluyveromyces lactis killer toxin were identified. Among these, eight were earlier identified to have a defect in formation of the mcm(5) side chain. Analysis of the remaining mutants and other known gamma-toxin resistant mutants revealed that sit4, kti14, and KTI5 mutants also have a defect in the formation of mcm(5). A mutant lacking two of the Sit4-associated proteins, Sap185 and Sap190, displays the same modification defect as a sit4-null mutant. Interestingly, several mutants were found to be defective in the synthesis of the 2-thio (s(2)) group of the mcm(5)s(2)U nucleoside. In addition to earlier described mutants, formation of the s(2) group was also abolished in urm1, uba4, and ncs2 mutants and decreased in the yor251c mutant. Like the absence of the mcm(5) side chain, the lack of the s(2) group renders tRNA(mcm5s2UUC Glu) less sensitive to gamma-toxin, reinforcing the importance of the wobble nucleoside mcm(5)s(2)U for tRNA cleavage by gamma-toxin.
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Affiliation(s)
- Bo Huang
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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26
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Zabel R, Bär C, Mehlgarten C, Schaffrath R. Yeast alpha-tubulin suppressor Ats1/Kti13 relates to the Elongator complex and interacts with Elongator partner protein Kti11. Mol Microbiol 2008; 69:175-87. [PMID: 18466297 DOI: 10.1111/j.1365-2958.2008.06273.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The alpha-tubulin suppressor 1 (ATS1) gene and the killer toxin-insensitive 13 (KTI13) locus from Saccharomyces cerevisiae are allelic. The Ats1/Kti13 gene product interacts with the cell polarity factor Nap1 and promotes growth inhibition of S. cerevisiae by zymocin, a tRNAse toxin complex from Kluyveromyces lactis. Kti13 removal causes zymocin resistance, a trait that is typical of defects in the Elongator complex. Here, we show that Kti13 co-purifies with the Elongator partner protein Kti11 and that the Kti11 interaction, not the Nap1 partnership, requires the C-terminus of Kti13. Moreover, Kti13 functionally relates to roles of the Elongator complex in tRNA wobble uridine modification, tRNA suppression of nonsense (SUP4) and missense (SOE1) mutations and tRNA restriction by zymocin. Also, inactivation of Kti13 or Elongator rescues the thermosensitive growth defect of secretory mutants (sec2-59(ts), sec12-4(ts)), suggesting that Kti13 and Elongator affect secretion processes that depend on the GTP exchange factors Sec2 and Sec12 respectively. Distinct from tandem deletions in KTI13 and Elongator genes, a kti13Delta kti11Delta double deletion induces synthetic sickness or lethality. In sum, our data suggest that Kti13 and Kti11 support Elongator functions and that they both share Elongator-independent role(s) that are important for cell viability.
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Affiliation(s)
- René Zabel
- Biologicum, Institut für Biologie, Institutsbereich Genetik, Martin-Luther-Universität, Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany
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27
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Svejstrup JQ. Elongator complex: how many roles does it play? Curr Opin Cell Biol 2007; 19:331-6. [PMID: 17466506 DOI: 10.1016/j.ceb.2007.04.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 04/12/2007] [Indexed: 11/29/2022]
Abstract
The multi-subunit Elongator complex was first identified by its association with an RNA polymerase II holoenzyme engaged in transcriptional elongation, and subsequent data have provided further evidence that the complex is involved in histone acetylation and transcription. However, most Elongator is cytoplasmic, and recent data has indicated a role in processes as diverse as exocytosis and tRNA modification. One of the subunits of Elongator is encoded by a gene that is mutated in patients suffering from the severe neurodevelopmental disorder familial dysautonomia.
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Affiliation(s)
- Jesper Q Svejstrup
- Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, EN6 3LD, UK.
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28
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Grasser KD. Emerging role for transcript elongation in plant development. TRENDS IN PLANT SCIENCE 2005; 10:484-90. [PMID: 16150628 DOI: 10.1016/j.tplants.2005.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 08/04/2005] [Accepted: 08/24/2005] [Indexed: 05/04/2023]
Abstract
Transcript elongation by RNA polymerase II (RNAPII), once regarded as the simple extension of the initiated mRNA, is a complex and highly regulated phase of the transcription cycle. Many factors have been identified that contribute to the dynamic control of the elongation stage of transcription. There are elongation factors that modulate the activity of RNAPII and other factors that facilitate the transcription through chromatin. Recent studies of mutants defective in elongation factors have revealed the importance of proper transcript elongation for the development of higher eukaryotes. Here, the essentials of transcript elongation are briefly summarized to discuss its role in developmental processes.
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Affiliation(s)
- Klaus D Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
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